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Shetti D, Mallela VR, Ye W, Sharif M, Ambrozkiewicz F, Trailin A, Liška V, Hemminki K. Emerging role of circulating cell-free RNA as a non-invasive biomarker for hepatocellular carcinoma. Crit Rev Oncol Hematol 2024; 200:104391. [PMID: 38795877 DOI: 10.1016/j.critrevonc.2024.104391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/30/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a severe neoplastic disease associated with high morbidity and mortality rates. HCC is often detected at advanced stages leading to ineffective curative treatments. Recently, liquid biopsy has emerged as a non-invasive method to identify highly specific HCC biomarkers in bodily fluids such as blood, serum, urine, and saliva. Circulating cell-free nucleic acids (cfNAs), particularly cell-free DNA (cfDNA) and cell-free RNA (cfRNA), have become promising candidates for biomarkers in liquid biopsy applications. While cfDNA presented significant challenges, researchers have turned their attention to cfRNA, which can be efficiently identified through various methods and is considered a potential biomarker for cancer diagnosis and prognosis. This review primarily focuses on studies related to detecting various cfRNA in body fluids as biomarkers. The aim is to provide a summary of available information to assist researchers in their investigations and the development of new diagnostic and prognostic tools.
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Affiliation(s)
- Dattatrya Shetti
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic.
| | - Venkata Ramana Mallela
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Wenjing Ye
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Mahyar Sharif
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University,Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Filip Ambrozkiewicz
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Andriy Trailin
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Václav Liška
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic; Department of Surgery, University Hospital in Pilsen and Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, Pilsen 323 00, Czech Republic
| | - Kari Hemminki
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic; Department of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
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2
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Thakur C, Qiu Y, Pawar A, Chen F. Epigenetic regulation of breast cancer metastasis. Cancer Metastasis Rev 2024; 43:597-619. [PMID: 37857941 DOI: 10.1007/s10555-023-10146-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Breast cancer is the most frequently diagnosed malignancy and the second leading cause of cancer-related mortality among women worldwide. Recurrent metastasis is associated with poor patient outcomes and poses a significant challenge in breast cancer therapies. Cancer cells adapting to a new tissue microenvironment is the key event in distant metastasis development, where the disseminating tumor cells are likely to acquire genetic and epigenetic alterations during the process of metastatic colonization. Despite several decades of research in this field, the exact mechanisms governing metastasis are not fully understood. However, emerging body of evidence indicates that in addition to genetic changes, epigenetic reprogramming of cancer cells and the metastatic niche are paramount toward successful metastasis. Here, we review and discuss the latest knowledge about the salient attributes of metastasis and epigenetic regulation in breast cancer and crucial research domains that need further investigation.
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Affiliation(s)
- Chitra Thakur
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA.
| | - Yiran Qiu
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Aashna Pawar
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Fei Chen
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA.
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3
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Bleckman RF, Haag CMSC, Rifaela N, Beukema G, Mathijssen RHJ, Steeghs N, Gelderblom H, Desar IME, Cleven A, Ter Elst A, Schuuring E, Reyners AKL. Levels of circulating tumor DNA correlate with tumor volume in gastro-intestinal stromal tumors: an exploratory long-term follow-up study. Mol Oncol 2024. [PMID: 38790141 DOI: 10.1002/1878-0261.13644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/26/2024] [Accepted: 03/15/2024] [Indexed: 05/26/2024] Open
Abstract
Patients with gastro-intestinal stromal tumors (GISTs) undergoing tyrosine kinase inhibitor therapy are monitored with regular computed tomography (CT) scans, exposing patients to cumulative radiation. This exploratory study aimed to evaluate circulating tumor DNA (ctDNA) testing to monitor treatment response and compare changes in ctDNA levels with RECIST 1.1 and total tumor volume measurements. Between 2014 and 2021, six patients with KIT proto-oncogene, receptor tyrosine kinase (KIT) exon-11-mutated GIST from whom long-term plasma samples were collected prospectively were included in the study. ctDNA levels of relevant plasma samples were determined using the KIT exon 11 digital droplet PCR drop-off assay. Tumor volume measurements were performed using a semi-automated approach. In total, 94 of 130 clinically relevant ctDNA samples were analyzed. Upon successful treatment response, ctDNA became undetectable in all patients. At progressive disease, ctDNA was detectable in five out of six patients. Higher levels of ctDNA correlated with larger tumor volumes. Undetectable ctDNA at the time of progressive disease on imaging was consistent with lower tumor volumes compared to those with detectable ctDNA. In summary, ctDNA levels seem to correlate with total tumor volume at the time of progressive disease. Our exploratory study shows promise for including ctDNA testing in treatment follow-up.
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Affiliation(s)
- Roos F Bleckman
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Charlotte M S C Haag
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Naomi Rifaela
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Gerrieke Beukema
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Neeltje Steeghs
- Department of Medical Oncology, The Netherlands Cancer Institute Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, The Netherlands
| | - Ingrid M E Desar
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen Cleven
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
- Department of Medical Oncology, Leiden University Medical Center, The Netherlands
| | - Arja Ter Elst
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ed Schuuring
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Anna K L Reyners
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
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4
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Rendek T, Pos O, Duranova T, Saade R, Budis J, Repiska V, Szemes T. Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics. Cancers (Basel) 2024; 16:2001. [PMID: 38893121 PMCID: PMC11171112 DOI: 10.3390/cancers16112001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation's origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics.
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Affiliation(s)
- Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Ondrej Pos
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | | | - Rami Saade
- 2nd Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Tomas Szemes
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
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5
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Padullés B, Carrasco R, Ingelmo-Torres M, Roldán FL, Gómez A, Vélez E, Alfambra H, Figueras M, Carrion A, Gil-Vernet J, Mengual L, Izquierdo L, Alcaraz A. Prognostic Value of Liquid-Biopsy-Based Biomarkers in Upper Tract Urothelial Carcinoma. Int J Mol Sci 2024; 25:3695. [PMID: 38612507 PMCID: PMC11012136 DOI: 10.3390/ijms25073695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Currently, there are no reliable prognostic factors to determine which upper tract urothelial carcinoma (UTUC) patients will progress after radical nephroureterectomy (RNU). We aim to evaluate whether liquid-biopsy-based biomarkers (circulating tumor cells (CTCs), cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA)) were able to predict clinical outcomes in localized UTUC patients undergoing RNU. Twenty patients were prospectively enrolled between 2021 and 2023. Two blood samples were collected before RNU and three months later. CTCs and cfDNA were isolated and evaluated using the IsoFlux system and Quant-iT PicoGreen dsDNA kit, respectively. Droplet digital PCR was performed to determine ctDNA status. Cox regression analysis was performed on CTCs, cfDNA, and ctDNA at two different follow-up time points to examine their influence on tumor progression and cancer-specific survival (CSS). During a median follow-up of 18 months, seven (35%) patients progressed and three (15%) died. Multivariate analysis demonstrated that cfDNA levels three months after RNU are a significant predictor of tumor progression (HR = 1.085; p = 0.006) and CSS (HR = 1.168; p = 0.029). No associations were found between CTC enumeration and ctDNA status with any of the clinical outcomes evaluated. The evaluation of cfDNA levels in clinical practice could improve the disease management of UTUC patients.
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Affiliation(s)
- Bernat Padullés
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
- Genètica i Tumors Urològics, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina I Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Raquel Carrasco
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
- Genètica i Tumors Urològics, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Mercedes Ingelmo-Torres
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
- Genètica i Tumors Urològics, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Fiorella L. Roldán
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
- Genètica i Tumors Urològics, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Ascensión Gómez
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
| | - Elena Vélez
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
| | - Héctor Alfambra
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
| | - Marcel Figueras
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
- Genètica i Tumors Urològics, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Albert Carrion
- Department of Urology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain
| | - Jordi Gil-Vernet
- Department of Urology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain
| | - Lourdes Mengual
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
- Genètica i Tumors Urològics, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina I Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Laura Izquierdo
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
- Genètica i Tumors Urològics, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Departament de Cirurgia i Especialitats Medicoquirúrgiques, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Antonio Alcaraz
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (B.P.); (L.M.)
- Genètica i Tumors Urològics, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Departament de Cirurgia i Especialitats Medicoquirúrgiques, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
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6
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Huang CC, Tsai YF, Liu CY, Lien PJ, Lin YS, Chao TC, Feng CJ, Chen YJ, Lai JI, Cheng HF, Chen BF, Hsu CY, Chiu JH, Tseng LM. Concordance of Targeted Sequencing from Circulating Tumor DNA and Paired Tumor Tissue for Early Breast Cancer. Cancers (Basel) 2023; 15:4475. [PMID: 37760445 PMCID: PMC10526508 DOI: 10.3390/cancers15184475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
In this study, we evaluated the concordance of targeted sequencing between paired ctDNA and matched tumor samples from early breast cancers treated with curative intention. Molecular profiling was performed using the Oncomine Comprehensive Assay v3 and the Oncomine Breast cfDNA Assay v2. The liquid biopsy detection rate was 39% (all-stage breast cancers, n = 612). Among 246 early-stage patients assayed for both ctDNA and matched tumor, the cfDNA assay detected 73 (29.6%) and the comprehensive assay detected 201 (81.7%) breast cancers with at least one alteration (χ2 test, p = 0.001). In total, 67 (25.6%) cases tested positive on both platforms, while the cfDNA and comprehensive assays detected an additional 10 (4%) and 138 (56%) cases, respectively. The most prevalent mutant genes were TP53 (68.3%) and KRAS (53.5%), while the PIK3CA (39.4%), AKT1 (45.9%), and ERBB2 (17.1%) mutations constituted biomarkers for FDA-approved therapeutics. Our study showed that tumor tissue should be the source of actionable mutation detection for early breast cancers, considering that the concordance rate between tumor and liquid biopsy was only one-quarter.
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Affiliation(s)
- Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Fang Tsai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Chun-Yu Liu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yen-Shu Lin
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Ta-Chung Chao
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Division of Chemotherapy, Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chin-Jung Feng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yen-Jen Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Jiun-I Lai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan
| | - Han-Fang Cheng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Bo-Fang Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chih-Yi Hsu
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Traditional Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
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7
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Karimi F, Azadbakht O, Veisi A, Sabaghan M, Owjfard M, Kharazinejad E, Dinarvand N. Liquid biopsy in ovarian cancer: advantages and limitations for prognosis and diagnosis. Med Oncol 2023; 40:265. [PMID: 37561363 DOI: 10.1007/s12032-023-02128-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023]
Abstract
Ovarian cancer (OC) is a highly fatal gynecologic malignancy, often diagnosed at an advanced stage which presents significant challenges for disease management. The clinical application of conventional tissue biopsy methods and serological biomarkers has limitations for the diagnosis and prognosis of OC patients. Liquid biopsy is a novel sampling method that involves analyzing distinctive tumor elements secreted into the peripheral blood. Growing evidence suggests that liquid biopsy methods such as circulating tumor cells, cell-free RNA, circulating tumor DNA, exosomes, and tumor-educated platelets may improve early prognosis and diagnosis of OC, leading to enhanced therapeutic management of the disease. This study reviewed the evidence demonstrating the utility of liquid biopsy components in OC prognosis and diagnosis, and evaluated the current advantages and limitations of these methods. Additionally, the existing obstacles and crucial topics for future studies utilizing liquid biopsy in OC patients were discussed.
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Affiliation(s)
- Farzaneh Karimi
- Department of Physiology, Behbahan Faculty of Medical Sciences, Behbahan, Iran.
| | - Omid Azadbakht
- Department of Radiology Technology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Ali Veisi
- Department of Physiology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Mohammad Sabaghan
- Department of Parasitology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Maryam Owjfard
- Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz University of Applied Science and Technology (UAST), Shiraz, Iran
| | | | - Negar Dinarvand
- Hyperlipidemia Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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8
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Kusaka M, Kawai A, Takahara K, Sasaki H, Ito T, Kenmochi T, Shiroki R. Total Cell-Free DNA as a Noninvasive Biomarker of a Delayed Graft Function After Kidney Transplantation From Donors After Cardiac Death. Transplant Proc 2023:S0041-1345(23)00141-0. [PMID: 37031037 DOI: 10.1016/j.transproceed.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/13/2023] [Indexed: 04/09/2023]
Abstract
BACKGROUND Because of the organ shortage, donation after cardiac death (DCD) kidney transplantation (KTx) is an alternative way of achieving KTx using brain-dead donors (BDs). Although the prognosis of DCD-KTx is improving, the graft suffers from delayed graft function (DGF), the management of which is essential. With progress in understanding the characteristics of cell-free DNA (CF-DNA), we consider plasma total CF-DNA (tCF-DNA) to be a useful biomarker for predicting DGF in DCD-KTx. STUDY DESIGN AND METHOD Consecutive patients from living donors (LDs; n = 9), BDs (n = 8), or DCD donors (n = 13) were enrolled. Plasma samples were collected after KTx and on postoperative days 3 and 5. CF-DNA was isolated, and tCF-DNA was quantified using the TapeStation 2200 software program. RESULTS The tCF-DNA levels after BD-KTx and DCD-KTx were higher than those after LD-KTx (LD, 78 ± 27 (ng/mL); BD, 99 ± 20; DCD, 150 ± 23); the difference between DCD-KTx and LD-KTx was statistically significant (P < .05). The tCF-DNA levels declined at postoperative day 5 (LD, 45 ± 10; BD, 51 ± 11; DCD, 66 ± 13). tCF-DNA levels were significantly increased in patients with DGF after KTx (DGF, 139 ± 22; immediate function, 91 ± 18; P < .05). The tCF-DNA level was correlated with the duration of DGF (r = 0.5825, P < .05). CONCLUSION Although the mechanism underlying DNA release from transplanted grafts into the recipient circulation remains unclear, cell death by apoptosis or necrosis and the active secretion of the immune system may play important roles in DGF. These data suggest that monitoring tCF-DNA may help predict graft recovery after DCD-KTx.
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Affiliation(s)
- Mamoru Kusaka
- Department of Urology, Fujita Health University Okazaki Medical Center, Okazaki, Aichi, Japan; Department of Urology, Fujita Health University, Toyoake , Aichi, Japan.
| | - Akihiro Kawai
- Department of Urology, Fujita Health University Okazaki Medical Center, Okazaki, Aichi, Japan; Department of Urology, Fujita Health University, Toyoake , Aichi, Japan
| | - Kiyoshi Takahara
- Department of Urology, Fujita Health University, Toyoake , Aichi, Japan
| | - Hitomi Sasaki
- Department of Urology, Fujita Health University, Toyoake , Aichi, Japan
| | - Taihei Ito
- Department of Organ Transplant Surgery, Fujita Health University, Toyoake , Aichi, Japan
| | - Takashi Kenmochi
- Department of Organ Transplant Surgery, Fujita Health University, Toyoake , Aichi, Japan
| | - Ryoichi Shiroki
- Department of Urology, Fujita Health University, Toyoake , Aichi, Japan
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9
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Hanna M, Dey N, Grady WM. Emerging Tests for Noninvasive Colorectal Cancer Screening. Clin Gastroenterol Hepatol 2023; 21:604-616. [PMID: 36539002 PMCID: PMC9974876 DOI: 10.1016/j.cgh.2022.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC) is among the most common cancers globally and a major cause of cancer-related deaths. The American Cancer Society estimates that CRC will kill 1 in 60 Americans, and CRC screening is recommended for all Americans ≥45 years of age. Current CRC screening methods are effective for preventing CRC and have been shown to reduce CRC-related mortality. However, none of the currently available tests is ideal, and many people are not compliant with screening recommendations. Novel screening tests based on advances in CRC molecular biology, genetics, and epigenetics, combined with developments in sequencing technologies and computational analytic methods, have been developed to address the shortcomings of current CRC screening tests. These emerging tests include blood-based assays that use plasma-derived circulating tumor DNA and serum proteins to detect early CRC and advanced adenomas, assays that use stool DNA or mRNA, and methods for profiling the gut microbiome. Here we review current screening modalities, and we discuss the principles behind the most promising emerging CRC screening tests and the data supporting their potential to be used in clinical practice.
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Affiliation(s)
- Marina Hanna
- Department of Medicine, University of Washington, Seattle, Washington
| | - Neelendu Dey
- Department of Medicine, University of Washington, Seattle, Washington; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington; Microbiome Research Initiative, Fred Hutchinson Cancer Center, Seattle, Washington.
| | - William M Grady
- Department of Medicine, University of Washington, Seattle, Washington; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington.
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10
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Abramson DH, Mandelker DL, Brannon AR, Dunkel IJ, Benayed R, Berger MF, Arcila ME, Ladanyi M, Friedman DN, Jayakumaran G, Diosdado MS, Robbins MA, Haggag-Lindgren D, Shukla N, Walsh MF, Kothari P, Tsui DWY, Francis JH. Mutant-RB1 circulating tumor DNA in the blood of unilateral retinoblastoma patients: What happens during enucleation surgery: A pilot study. PLoS One 2023; 18:e0271505. [PMID: 36735656 PMCID: PMC9897525 DOI: 10.1371/journal.pone.0271505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Cell free DNA (cfDNA) and circulating tumor cell free DNA (ctDNA) from blood (plasma) are increasingly being used in oncology for diagnosis, monitoring response, identifying cancer causing mutations and detecting recurrences. Circulating tumor RB1 DNA (ctDNA) is found in the blood (plasma) of retinoblastoma patients at diagnosis before instituting treatment (naïve). We investigated ctDNA in naïve unilateral patients before enucleation and during enucleation (6 patients/ 8 mutations with specimens collected 5-40 minutes from severing the optic nerve) In our cohort, following transection the optic nerve, ctDNA RB1 VAF was measurably lower than pre-enucleation levels within five minutes, 50% less within 15 minutes and 90% less by 40 minutes.
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Affiliation(s)
- David H. Abramson
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York, United States of America
- * E-mail:
| | - Diana L. Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - A. Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ira J. Dunkel
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pediatrics, Weill Cornell Medical Center, New York, New York, United States of America
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Danielle Novetsky Friedman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Monica S. Diosdado
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Melissa A. Robbins
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dianna Haggag-Lindgren
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael F. Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Prachi Kothari
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dana W. Y. Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Jasmine H. Francis
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York, United States of America
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11
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Kletke SN, Soliman S, Racher H, Mallipatna A, Shaikh F, Mireskandari K, Gallie BL. A typical anterior retinoblastoma: diagnosis by aqueous humor cell-free DNA analysis. Ophthalmic Genet 2022; 43:862-865. [PMID: 36326029 DOI: 10.1080/13816810.2022.2141800] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Aqueous humor from eyes with active retinoblastoma contains tumor-derived cell-free DNA. MATERIALS AND METHODS Single retrospective case report. RESULTS A 13-year-old girl with acute right eye pain and redness was diagnosed with hypertensive anterior uveitis. Following initial management, she was referred to ocular oncology for an atypical clinical picture. Multiple seeds were noted 360 degrees in the anterior chamber, at the equator of the lens and canal of Petit, and ultrasound biomicroscopy identified a temporal pars plana lesion. While aqueous humor cytology was inconclusive for malignancy, targeted next-generation sequencing of aqueous cell-free DNA identified biallelic RB1 full gene deletion, confirming the diagnosis of retinoblastoma. Partial regression followed three cycles of systemic carboplatin, etoposide, and vincristine and three intracameral melphalan injections. Four months later, she had recurrence of the primary tumor and increase in seeding and received the investigational sustained release episcleral topotecan chemoplaque. Stable regression was achieved to 28-month follow-up, with no detectable aqueous cell-free DNA. CONCLUSIONS RB1 sequencing analysis of tumor-derived cell-free DNA from aqueous humor can confirm the diagnosis of retinoblastoma in cases of diagnostic uncertainty.
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Affiliation(s)
- Stephanie N Kletke
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Sameh Soliman
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Hilary Racher
- Scientific and Laboratory Operations, Dynacare/Impact Genetics, Brampton, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Ashwin Mallipatna
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Furqan Shaikh
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada.,Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Kamiar Mireskandari
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Brenda L Gallie
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
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12
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Hatipoğlu T, Esmeray Sönmez E, Hu X, Yuan H, Danyeli AE, Şeyhanlı A, Önal-Süzek T, Zhang W, Akman B, Olgun A, Özkal S, Alacacıoğlu İ, Özcan MA, You H, Küçük C. Plasma Concentrations and Cancer-Associated Mutations in Cell-Free Circulating DNA of Treatment-Naive Follicular Lymphoma for Improved Non-Invasive Diagnosis and Prognosis. Front Oncol 2022; 12:870487. [PMID: 35795062 PMCID: PMC9252432 DOI: 10.3389/fonc.2022.870487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/02/2022] [Indexed: 12/14/2022] Open
Abstract
Follicular lymphoma (FL) is the second most frequent non-Hodgkin lymphoma accounting for 10-20% of all lymphomas in western countries. As a clinically heterogeneous cancer, FL occasionally undergoes histological transformation to more aggressive B cell lymphoma types that are associated with poor prognosis. Here we evaluated the potential of circulating cell-free DNA (cfDNA) to improve the diagnosis and prognosis of follicular lymphoma patients. Twenty well-characterized FL cases (13 symptomatic and 7 asymptomatic) were prospectively included in this study. Plasma cfDNA, formalin-fixed paraffin-embedded (FFPE) tumor tissue DNA, and patient-matched granulocyte genomic DNA samples were obtained from 20 treatment-naive FL cases. Ultra-deep targeted next-generation sequencing was performed with these DNA samples by using a custom-designed platform including exons and exon-intron boundaries of 110 FL related genes. Using a strict computational bioinformatics pipeline, we identified 91 somatic variants in 31 genes in treatment-naive FL cases. Selected variants were cross-validated by using PCR-Sanger sequencing. We observed higher concentrations of cfDNA and a higher overlap of somatic variants present both in cfDNA and tumor tissue DNA in symptomatic FL cases compared to asymptomatic ones. Variants known to be associated with FL pathogenesis such as STAT6 p.D419 or EZH2 p.Y646 were observed in patient-matched cfDNA and tumor tissue samples. Consistent with previous observations, high Ki-67 staining, elevated LDH levels, FDG PET/CT positivity were associated with poor survival. High plasma cfDNA concentrations or the presence of BCL2 mutations in cfDNA showed significant association with poor survival in treatment-naive patients. BCL2 mutation evaluations in cfDNA improved the prognostic utility of previously established variables. In addition, we observed that a FL patient who had progressive disease contained histological transformation-associated gene (i.e. B2M and BTG1) mutations only in cfDNA. Pre-treatment concentrations and genotype of plasma cfDNA may be used as a liquid biopsy to improve diagnosis, risk stratification, and prediction of histological transformation. Targeted therapies related to oncogenic mutations may be applied based on cfDNA genotyping results. However, the results of this study need to be validated in a larger cohort of FL patients as the analyses conducted in this study have an exploratory nature.
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Affiliation(s)
- Tevfik Hatipoğlu
- İzmir Biomedicine and Genome Center, İzmir, Turkey
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
| | - Esra Esmeray Sönmez
- İzmir Biomedicine and Genome Center, İzmir, Turkey
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
| | - Xiaozhou Hu
- İzmir Biomedicine and Genome Center, İzmir, Turkey
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
| | - Hongling Yuan
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
| | - Ayça Erşen Danyeli
- Department of Pathology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Ahmet Şeyhanlı
- Department of Hematology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Tuğba Önal-Süzek
- Department of Bioinformatics, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Weiwei Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Burcu Akman
- İzmir Biomedicine and Genome Center, İzmir, Turkey
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
| | - Aybüke Olgun
- Department of Hematology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Sermin Özkal
- Department of Pathology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - İnci Alacacıoğlu
- Department of Hematology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Mehmet Ali Özcan
- Department of Hematology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Hua You
- Department of Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Can Küçük, ; Hua You,
| | - Can Küçük
- İzmir Biomedicine and Genome Center, İzmir, Turkey
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
- *Correspondence: Can Küçük, ; Hua You,
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13
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Wu HJ, Chu PY. Current and Developing Liquid Biopsy Techniques for Breast Cancer. Cancers (Basel) 2022; 14:2052. [PMID: 35565189 PMCID: PMC9105073 DOI: 10.3390/cancers14092052] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and leading cause of cancer mortality among woman worldwide. The techniques of diagnosis, prognosis, and therapy monitoring of breast cancer are critical. Current diagnostic techniques are mammography and tissue biopsy; however, they have limitations. With the development of novel techniques, such as personalized medicine and genetic profiling, liquid biopsy is emerging as the less invasive tool for diagnosing and monitoring breast cancer. Liquid biopsy is performed by sampling biofluids and extracting tumor components, such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free mRNA (cfRNA) and microRNA (miRNA), proteins, and extracellular vehicles (EVs). In this review, we summarize and focus on the recent discoveries of tumor components and biomarkers applied in liquid biopsy and novel development of detection techniques, such as surface-enhanced Raman spectroscopy (SERS) and microfluidic devices.
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Affiliation(s)
- Hsing-Ju Wu
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua 505, Taiwan
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Pei-Yi Chu
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
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14
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Elzehery R, Effat N, El Farahaty R, Elsayed Farag R, Abo-Hashem EM, Elhelaly R. Circulating Cell-Free DNA and DNA Integrity as Molecular Diagnostic Tools in Hepatocellular Carcinoma. Am J Clin Pathol 2022; 158:254-262. [PMID: 35403666 DOI: 10.1093/ajcp/aqac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/02/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES We assessed the ability to use circulating cell-free DNA (cfDNA) and the DNA integrity index (DNAII) to detect the transition from liver cirrhosis (LC) to hepatocellular carcinoma (HCC). METHODS Circulating cfDNA and DNAII were measured in 50 patients with advanced LC and 50 patients with HCC who were followed for 1 month after transarterial chemoembolization (TACE). Fifty healthy participants served as a control group. Real-time quantitative polymerase chain reaction (PCR) was used to measure circulating cfDNA concentration, and Alu-PCR was used to measure the concentration of Alu repeats, both short fragments (115 base pairs [bp]) and long fragments (247 bp). We compared liquid biopsy results with the relevant traditional markers. RESULTS The HCC group showed significantly higher circulating cfDNA concentrations and DNAII values compared with the LC and control groups. No significant differences were found in circulating cfDNA concentrations and DNAII values between the LC and control groups. Circulating cfDNA concentrations decreased significantly after treatment (TACE); areas under the curve of circulating cfDNA concentration and DNAII values were significantly better than those of ɑ-fetoprotein and vascular endothelial growth factor in discriminating between LC and HCC. CONCLUSIONS The combined use of DNAII with proteins induced by vitamin K absence or antagonist showed better diagnostic performance in HCC. Circulating cfDNA could have a potential role in monitoring HCC treatment.
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Affiliation(s)
| | - Narmin Effat
- Department of Clinical Pathology, Mansoura, Egypt
| | | | - Raghda Elsayed Farag
- Department of Tropical Medicine, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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15
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Abstract
Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism. IMPORTANCE With advances in metagenomic sequencing, the microbial composition of diverse environmental systems has been investigated, providing new perspectives on potential ecological dynamics and dimensions for experimental investigations. Here, we characterized exocellular free DNA via metagenomics, using a newly developed method that separates free DNA from cells, viruses, and vesicles, and facilitated the independent characterization of each fraction. The fate of this free DNA has both ecological consequences as a nutrient (N and P) source and potential evolutionary consequences as a source of genetic transformation. Here, we document different microbial sources of free DNA at the surface (0 to 200 m) versus depths of 250 to 1,000 m, suggesting that distinct free DNA production mechanisms may be present throughout the oligotrophic water column. Examining microbial processes through the lens of exocellular DNA provides insights into the production of labile dissolved organic matter (i.e., free DNA) at the surface (likely by viral lysis) and processes that influence the fate of sinking, surface-derived organic matter.
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16
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Johansson G, Berndsen M, Lindskog S, Österlund T, Fagman H, Muth A, Ståhlberg A. Monitoring Circulating Tumor DNA During Surgical Treatment in Patients with Gastrointestinal Stromal Tumors. Mol Cancer Ther 2021; 20:2568-2576. [PMID: 34552011 PMCID: PMC9398151 DOI: 10.1158/1535-7163.mct-21-0403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 09/14/2021] [Indexed: 01/07/2023]
Abstract
The majority of patients diagnosed with advanced gastrointestinal stromal tumors (GISTs) are successfully treated with a combination of surgery and tyrosine kinase inhibitors (TKIs). However, it remains challenging to monitor treatment efficacy and identify relapse early. Here, we utilized a sequencing strategy based on molecular barcodes and developed a GIST-specific panel to monitor tumor-specific and TKI resistance mutations in cell-free DNA and applied the approach to patients undergoing surgical treatment. Thirty-two patients with GISTs were included, and 161 blood plasma samples were collected and analyzed at routine visits before and after surgery and at the beginning, during, and after surgery. Patients were included regardless of their risk category. Our GIST-specific sequencing approach allowed detection of tumor-specific mutations and TKI resistance mutations with mutant allele frequency < 0.1%. Circulating tumor DNA (ctDNA) was detected in at least one timepoint in nine of 32 patients, ranging from 0.04% to 93% in mutant allele frequency. High-risk patients were more often ctDNA positive than other risk groups (P < 0.05). Patients with detectable ctDNA also displayed higher tumor cell proliferation rates (P < 0.01) and larger tumor sizes (P < 0.01). All patients who were ctDNA positive during surgery became negative after surgery. Finally, in two patients who progressed on TKI treatment, we detected multiple resistance mutations. Our data show that ctDNA may become a clinically useful biomarker in monitoring treatment efficacy in patients with high-risk GISTs and can assist in treatment decision making.
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Affiliation(s)
- Gustav Johansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Marta Berndsen
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Section of Endocrine and Sarcoma Surgery, Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Stefan Lindskog
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Section of Endocrine and Sarcoma Surgery, Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Surgery, Halland Regional Hospital Varberg, Region Halland, Varberg, Sweden
| | - Tobias Österlund
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Henrik Fagman
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Andreas Muth
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Section of Endocrine and Sarcoma Surgery, Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Corresponding Authors: Anders Ståhlberg, Sahlgrenska Center for Cancer Research, University of Gothenburg, Box 425, Gothenburg 405 30, Sweden. E-mail: ; and Andreas Muth, Department of Surgery, Sahlgrenska University Hospital, Blå stråket 5, 413 45 Gothenburg, Sweden. E-mail:
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.,Corresponding Authors: Anders Ståhlberg, Sahlgrenska Center for Cancer Research, University of Gothenburg, Box 425, Gothenburg 405 30, Sweden. E-mail: ; and Andreas Muth, Department of Surgery, Sahlgrenska University Hospital, Blå stråket 5, 413 45 Gothenburg, Sweden. E-mail:
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17
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Vietri MT, D'Elia G, Benincasa G, Ferraro G, Caliendo G, Nicoletti GF, Napoli C. DNA methylation and breast cancer: A way forward (Review). Int J Oncol 2021; 59:98. [PMID: 34726251 DOI: 10.3892/ijo.2021.5278] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
The current management of breast cancer (BC) lacks specific non‑invasive biomarkers able to provide an early diagnosis of the disease. Epigenetic‑sensitive signatures are influenced by environmental exposures and are mediated by direct molecular mechanisms, mainly guided by DNA methylation, which regulate the interplay between genetic and non‑genetic risk factors during cancerogenesis. The inactivation of tumor suppressor genes due to promoter hypermethylation is an early event in carcinogenesis. Of note, targeted tumor suppressor genes are frequently hypermethylated in patient‑derived BC tissues and peripheral blood biospecimens. In addition, epigenetic alterations in triple‑negative BC, as the most aggressive subtype, have been identified. Thus, detecting both targeted and genome‑wide DNA methylation changes through liquid‑based assays appears to be a useful clinical strategy for early detection, more accurate risk stratification and a personalized prediction of therapeutic response in patients with BC. Of note, the DNA methylation profile may be mapped by isolating the circulating tumor DNA from the plasma as a more accessible biospecimen. Furthermore, the sensitivity to treatment with chemotherapy, hormones and immunotherapy may be altered by gene‑specific DNA methylation, suggesting novel potential drug targets. Recently, the use of epigenetic drugs administered alone and/or with anticancer therapies has led to remarkable results, particularly in patients with BC resistant to anticancer treatment. The aim of the present review was to provide an update on DNA methylation changes that are potentially involved in BC development and their putative clinical utility in the fields of diagnosis, prognosis and therapy.
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Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanna D'Elia
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuseppe Ferraro
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Gemma Caliendo
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanni Francesco Nicoletti
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
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18
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Krumbholz M, Eiblwieser J, Ranft A, Zierk J, Schmidkonz C, Stütz AM, Peneder P, Tomazou EM, Agaimy A, Bäuerle T, Hartmann W, Dirksen U, Metzler M. Quantification of Translocation-Specific ctDNA Provides an Integrating Parameter for Early Assessment of Treatment Response and Risk Stratification in Ewing Sarcoma. Clin Cancer Res 2021; 27:5922-5930. [PMID: 34426444 DOI: 10.1158/1078-0432.ccr-21-1324] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/05/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE We evaluated the predictive and prognostic value of circulating tumor DNA (ctDNA) in patients with Ewing sarcoma (EWS) treated in the EWING2008 trial. EXPERIMENTAL DESIGN Plasma samples from 102 patients with EWS enrolled in the EWING2008 trial were obtained before and during induction chemotherapy. Genomic EWSR1 fusion sequence spanning primers and probes were used for highly specific and sensitive quantification of the levels of ctDNA by digital droplet PCR. ctDNA levels were correlated to established clinical risk factors and outcome parameters. RESULTS Pretreatment ctDNA copy numbers were correlated with event-free and overall survival. The reduction in ctDNA levels below the detection limit was observed in most cases after only two blocks of vincristine, ifosfamide, doxorubicin, and etoposide (VIDE) induction chemotherapy. The persistence of ctDNA after two VIDE blocks was a strong predictor of poor outcomes. ctDNA levels correlated well with most established clinical risk factors; an inverse correlation was found only for the histologic response to induction therapy. ctDNA levels did not provide simple representations of tumor volume, but integrated information from various tumor characteristics represented an independent EWS tumor marker with predictive and prognostic value. CONCLUSIONS ctDNA copy number in the plasma of patients with EWS is a quantifiable parameter for early risk stratification and can be used as a dynamic noninvasive biomarker for early prediction of treatment response and outcome of patients.
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Affiliation(s)
- Manuela Krumbholz
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany. .,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Johanna Eiblwieser
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Andreas Ranft
- Pediatrics III, West German Cancer Centre, University Hospital of Essen, Essen, Germany
| | - Jakob Zierk
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | | | - Adrian M Stütz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter Peneder
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eleni M Tomazou
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Abbas Agaimy
- Department of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Tobias Bäuerle
- Department of Radiology, University Hospital Erlangen, Erlangen, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, University Hospital Muenster, Gerhard Domagk Institute of Pathology, Muenster, Germany
| | - Uta Dirksen
- Pediatrics III, West German Cancer Centre, University Hospital of Essen, Essen, Germany
| | - Markus Metzler
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany.,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
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19
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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20
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Martinez-Dominguez MV, Zottel A, Šamec N, Jovčevska I, Dincer C, Kahlert UD, Nickel AC. Current Technologies for RNA-Directed Liquid Diagnostics. Cancers (Basel) 2021; 13:5060. [PMID: 34680210 PMCID: PMC8534233 DOI: 10.3390/cancers13205060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
There is unequivocal acceptance of the variety of enormous potential liquid nucleic acid-based diagnostics seems to offer. However, the existing controversies and the increased awareness of RNA-based techniques in society during the current global COVID-19 pandemic have made the readiness of liquid nucleic acid-based diagnostics for routine use a matter of concern. In this regard-and in the context of oncology-our review presented and discussed the status quo of RNA-based liquid diagnostics. We summarized the technical background of the available assays and benchmarked their applicability against each other. Herein, we compared the technology readiness level in the clinical context, economic aspects, implementation as part of routine point-of-care testing as well as performance power. Since the preventive care market is the most promising application sector, we also investigated whether the developments predominantly occur in the context of early disease detection or surveillance of therapy success. In addition, we provided a careful view on the current biotechnology investment activities in this sector to indicate the most attractive strategies for future economic success. Taken together, our review shall serve as a current reference, at the interplay of technology, clinical use and economic potential, to guide the interested readers in this rapid developing sector of precision medicine.
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Affiliation(s)
| | - Alja Zottel
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Neja Šamec
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Ivana Jovčevska
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Can Dincer
- FIT Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79110 Freiburg, Germany;
- Laboratory for Sensors, Department of Microsystems Engineering—IMTEK, University of Freiburg, 79110 Freiburg, Germany
| | - Ulf Dietrich Kahlert
- Clinic for Neurosurgery, Medical Faculty, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.V.M.-D.); (U.D.K.)
- Molecular and Experimental Surgery, Clinic of General-, Visceral-, Vascular-, and Transplant Surgery, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Ann-Christin Nickel
- Clinic for Neurosurgery, Medical Faculty, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.V.M.-D.); (U.D.K.)
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21
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Stawski R, Stec-Martyna E, Chmielecki A, Nowak D, Perdas E. Current Trends in Cell-Free DNA Applications. Scoping Review of Clinical Trials. BIOLOGY 2021; 10:biology10090906. [PMID: 34571783 PMCID: PMC8468988 DOI: 10.3390/biology10090906] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023]
Abstract
We aimed to summarize the current knowledge about the trends in cfDNA application based on the analysis of clinical trials registered until April 2021. International Clinical Trials Registry Platform (ICTRP) and Clinicaltrials.gov were searched with the keywords: "cf-DNA"; "Circulating DNA"; "Deoxyribonucleic Acid"; and "Cell-Free Deoxyribonucleic Acid". Of 605 clinical trials, we excluded 237 trials, and 368 remaining ones were subject to further analysis. The subject, number of participants, and study design were analyzed. Our scoping review revealed three main trends: oncology (n = 255), non-invasive prenatal diagnostic (n = 48), and organ transplantation (n = 41), and many (n = 22) less common such as sepsis, sport, or autoimmune diseases in 368 clinical trials. Clinical trials are translating theory into clinical care. However, the diagnostic value of cfDNA remains controversial, and diagnostic accuracy still needs to be evaluated. Thus, further studies are necessary until cfDNA turns into a standard in clinical practice.
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Affiliation(s)
- Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
- Correspondence: (R.S.); (E.P.)
| | - Emilia Stec-Martyna
- Central Scientific Laboratory, Medical University of Lodz, 6/8 Mazowiecka St., 92-215 Lodz, Poland;
| | - Adam Chmielecki
- Sport Centre of the Medical University of Lodz, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Ewelina Perdas
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
- Correspondence: (R.S.); (E.P.)
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22
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Kamińska P, Buszka K, Zabel M, Nowicki M, Alix-Panabières C, Budna-Tukan J. Liquid Biopsy in Melanoma: Significance in Diagnostics, Prediction and Treatment Monitoring. Int J Mol Sci 2021; 22:9714. [PMID: 34575876 PMCID: PMC8468624 DOI: 10.3390/ijms22189714] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/25/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy is a common term referring to circulating tumor cells and other biomarkers, such as circulating tumor DNA (ctDNA) or extracellular vesicles. Liquid biopsy presents a range of clinical advantages, such as the low invasiveness of the blood sample collection and continuous control of the tumor progression. In addition, this approach enables the mechanisms of drug resistance to be determined in various methods of cancer treatment, including immunotherapy. However, in the case of melanoma, the application of liquid biopsy in patient stratification and therapy needs further investigation. This review attempts to collect all of the relevant and recent information about circulating melanoma cells (CMCs) related to the context of malignant melanoma and immunotherapy. Furthermore, the biology of liquid biopsy analytes, including CMCs, ctDNA, mRNA and exosomes, as well as techniques for their detection and isolation, are also described. The available data support the notion that thoughtful selection of biomarkers and technologies for their detection can contribute to the development of precision medicine by increasing the efficacy of cancer diagnostics and treatment.
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Affiliation(s)
- Paula Kamińska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Karolina Buszka
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Maciej Zabel
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Góra, 65-046 Zielona Góra, Poland;
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, 34093 Montpellier, France;
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Joanna Budna-Tukan
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
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23
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Chien TJ. A review of the endocrine resistance in hormone-positive breast cancer. Am J Cancer Res 2021; 11:3813-3831. [PMID: 34522451 PMCID: PMC8414389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023] Open
Abstract
Hormone-positive breast cancer (BC) is a unique heterogeneous disease with a favorable prognosis compared to other types of breast cancer. As tumor biology influences the prognosis and clinical treatment, a deep understanding of how the molecular mechanisms regulate hormone sensitivity or resistance is critical in improving the efficacy and overcoming the endocrine resistance. This article comprehensively reviews the endocrine resistance in hormone-positive BC from a molecular and genetic perspective, encompassing the updated treatment and developing direction. This review includes the mechanisms of hormone resistance, which vary from epigenetic changes, crosstalk between signaling networks, cell cycle aberrance, and even change in the tumor microenvironment (TME) or stem cell. These mechanisms may contribute to treatment resistance. Current targeted therapy for hormone-resistant tumors includes PI3K/AKT/mTOR and cdk4/6 inhibitors. Several relevant pathways, biomarkers, and predictor genes have also been identified. Immunotherapy so far has a relatively less crucial role in hormone-positive than in triple-negative BC. Furthermore, the methodology to identify the PDL1 is not standardized. In a molecule and gene study, next-generation sequencing with circulating tumor DNA (ctDNA) has recently appeared as a sensitive and minimally invasive tool worth investigating.
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Affiliation(s)
- Tsai-Ju Chien
- Division of Hemato-Oncology, Department of Internal Medicine, Branch of Zhong-Zhou, Taipei City HospitalTaipei, Taiwan
- Division of Hemato-Oncology, Department of Internal Medicine, Branch of Jen-Ai, Taipei City HospitalTaipei, Taiwan
- Institute of Traditional Medicine, National Yang-Ming Chiao Tung UniversityTaipei, Taiwan
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24
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The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes. Surgeon 2021; 20:e163-e173. [PMID: 34362650 DOI: 10.1016/j.surge.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Liquid biopsy is gaining increasing clinical utility in the management of cancer patients. The main components of a liquid biopsy are circulating nucleic acids, circulating tumour cells and extracellular vesicles such as exosomes. Circulating nucleic acids including cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) in particular have been the focus of recent attention as they have demonstrated excellent potential in cancer screening, provision of prognostic information and in genomic profiling of a tumour without the need for repeated tissue biopsies. The aim of this review was to explore the current evidence in relation to the use of liquid biopsy in the perioperative setting and identify ways in which liquid biopsy may be applied in the future. METHODS This narrative review is based on a comprehensive literature search up to the 1st of June 2020 for papers relevant to the application of liquid biopsy in surgical oncology, focusing particularly on the perioperative period. RESULTS Recent evidence has demonstrated that perioperative liquid biopsy can accurately stratify patients' risk of recurrence compared to conventional biomarkers. Attention to the perioperative dynamics of liquid biopsy components can potentially provide new understanding of the complex relationship between surgery and cancer outcome. In addition, careful evaluation of liquid biopsy components in the perioperative window may provide important diagnostic and therapeutic information for cancer patients. CONCLUSION The rapidly evolving concept of the liquid biopsy has the potential to become the cornerstone for decision making around surveillance and adjuvant therapies the era of personalised medicine.
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25
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Yang CS, Kim IH, Chae HD, Kim DD, Jeon CH. Detection of Circulating Gastrointestinal Cancer Cells in Conditionally Reprogrammed Cell Culture. In Vivo 2021; 35:1515-1520. [PMID: 33910829 DOI: 10.21873/invivo.12404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND/AIM The aim of this study was to detect circulating tumor cells (CTC) in the peripheral blood of gastrointestinal cancer patients using conditionally reprogrammed cell (CRC) culture. MATERIALS AND METHODS We confirmed the sensitivity of the CRC culture method. Five ml of blood were obtained from 81 cancer patients (56 colorectal and 25 gastric). The collected mononuclear cells were cultured for 4 weeks in the CRC condition. Finally, cultured cells were characterized by RT-PCR for the expression of hTERT and MAGE A1-6 mRNA. RESULTS The CRC method had a CTC detection limit of 6 cells for gastric cancer cells. After culture of 81 blood specimens, 38 formed visible cells, including 5 colonies. Among the 38 cells, 13 were hTERT positive and 4 were MAGE A1-6 positive. The final CTC detection rate was 16.0%. CONCLUSION The CRC culture may potentially be used to evaluate the metastatic cancer cells in the circulation.
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Affiliation(s)
- Chun-Seok Yang
- Department of General Surgery, Medical School, Daegu Catholic University Medical Center, Daegu, Republic of Korea
| | - In-Hwan Kim
- Department of General Surgery, Medical School, Daegu Catholic University Medical Center, Daegu, Republic of Korea
| | - Hyun-Dong Chae
- Department of General Surgery, Medical School, Daegu Catholic University Medical Center, Daegu, Republic of Korea
| | - Dae-Dong Kim
- Department of General Surgery, Medical School, Yonsei University, Seoul, Republic of Korea
| | - Chang-Ho Jeon
- Department of Laboratory Medicine, Medical School, Daegu Catholic University Medical Center, Daegu, Republic of Korea
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26
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Guillen A, Smallwood K, Killick DR. Molecular pathology in the cancer clinic - where are we now and where are we headed? J Small Anim Pract 2021; 62:507-520. [PMID: 33974272 DOI: 10.1111/jsap.13330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/14/2020] [Accepted: 03/04/2021] [Indexed: 11/29/2022]
Abstract
Molecular pathology is a developing sub-microscopic discipline of pathology that studies the effects of molecular variations and mutations on disease processes. The ultimate goal of molecular pathology in cancer is to predict risk, facilitate diagnosis and improve prognostication based on a complete understanding of the biological impact of specific molecular variations, mutations and dysregulations. This knowledge will provide the basis for customised cancer treatment, so-called precision medicine. Rapid developments in genomics have placed this field at the forefront of clinical molecular pathology and there are already a number of well-established genetic tests available for clinical use including PCR of antigen receptor rearrangement and KIT mutational analysis. Moving beyond tests assessing a single gene, there are significant research efforts utilising genomics to predict cancer risk, forecast aggressive behaviour and identify druggable mutations and therapeutic biomarkers. Researchers are also investigating the use of circulating cells and nucleic acid for clinically useful low morbidity genomic assessments. If we are to realise the full potential of molecular pathology and precision medicine there are a number of challenges to overcome. These include developing our understanding of the underlying biology (in particular intra-tumoural heterogeneity), methodological standardisation of assays, provision of adequate infrastructure and production of novel therapeutics backed by high-quality clinical data supporting the precision medicine approach. The era of molecular pathology holds the potential to revolutionise veterinary cancer care, but its impact on clinical practice will depend upon the extent to which the inherent challenges can be overcome.
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Affiliation(s)
- A Guillen
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Ln, Hatfield, AL9 7TA, UK
| | - K Smallwood
- Department of Small Animal Clinical Science, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst, Chester High Road, Neston, CH64 7TE, UK
| | - D R Killick
- Department of Small Animal Clinical Science, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst, Chester High Road, Neston, CH64 7TE, UK
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27
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González de Aledo-Castillo JM, Casanueva-Eliceiry S, Soler-Perromat A, Fuster D, Pastor V, Reguart N, Viñolas N, Reyes R, Vollmer I, Paredes P, Puig-Butillé JA. Cell-free DNA concentration and fragment size fraction correlate with FDG PET/CT-derived parameters in NSCLC patients. Eur J Nucl Med Mol Imaging 2021; 48:3631-3642. [PMID: 33797597 DOI: 10.1007/s00259-021-05306-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/07/2021] [Indexed: 01/26/2023]
Abstract
PURPOSE The aim of our study was to investigate the correlation between cfDNA concentration and fragment size fraction with FDG PET/CT- and CT-derived parameters in untreated NSCLC patient. METHODS Fifty-three patients diagnosed of locally advanced or metastatic NSCLC who had undergone FDG PET/CT, CT and cfDNA analysis prior to any treatment were included in this retrospective study. CfDNA concentration was measured by fluorometry and fragment size fractions were determined by microchip electrophoresis. [18F]F-FDG PET/CT was performed and standardised uptake values (SUV), metabolic tumour volume (MTV) and total lesion glycolysis (TLG) were calculated for primary, extrapulmonary and total disease. CT scans were evaluated according to RECIST 1.1 criteria. RESULTS CfDNA concentration showed a positive correlation with extrapulmonary MTV (r2 = 0.36, P = 0.009), and extrapulmonary TLG (r2 = 0.35, P = 0.009) and their whole-body (wb) ratios. Higher concentrations of total cfDNA were found in patients with liver lesions. Short fragments of cfDNA (100-250 bp) showed a positive correlation with extrapulmonary MTV (r2 = 0.49, P = 0.0005) and extrapulmonary TLG (r2 = 0.39, P = 0.006) and their respective wb ratios, and a negative correlation with SUVmean (r2 = -0.31, P = 0.03) and SUVmean/SUVmax ratio (r2 = -0.34, P = 0.02). A higher fraction of short cfDNA fragments was found in patients with liver and pleural lesions. CONCLUSIONS This study supports the hypothesis that cfDNA concentration and short cfDNA fragment size fraction reflect the tumour burden as well as metabolic activity in advanced NSCLC patients. This suggests their suitability as complementary tests for a more accurate diagnosis of tumour metabolic behaviour and to allow personalised therapies.
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Affiliation(s)
| | | | | | - D Fuster
- Nuclear Medicine Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - V Pastor
- Molecular Biology CORE, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - N Reguart
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,Medical Oncology Department, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - N Viñolas
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - R Reyes
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - I Vollmer
- Radiology Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
| | - P Paredes
- Nuclear Medicine Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - J A Puig-Butillé
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain. .,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain. .,Molecular Biology CORE, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain.
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Andersson D, Kristiansson H, Kubista M, Ståhlberg A. Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations. Expert Rev Mol Diagn 2021; 21:299-310. [PMID: 33683971 DOI: 10.1080/14737159.2021.1889371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation.Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications.Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Helena Kristiansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Kubista
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.,TATAA Biocenter, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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Abramson DH, Mandelker D, Francis JH, Dunkel IJ, Brannon AR, Benayed R, Berger MF, Arcila ME, Ladanyi M, Friedman DN, Jayakumaran G, Diosdado MS, Robbins MA, Haggag-Lindgren D, Shukla N, Walsh M, Kothari P, Tsui DW. Retrospective Evaluation of Somatic Alterations in Cell-Free DNA from Blood in Retinoblastoma. OPHTHALMOLOGY SCIENCE 2021; 1:100015. [PMID: 36246006 PMCID: PMC9560572 DOI: 10.1016/j.xops.2021.100015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 12/18/2022]
Abstract
Purpose Analysis of circulating tumor DNA (ctDNA) in the plasma of patients with retinoblastoma and simulating lesions. Design Retrospective cross-sectional study of the association of plasma ctDNA from retinoblastoma and simulating lesions with disease course. Participants Fifty-eight Memorial Sloan Kettering Cancer Center patients with retinoblastoma comprising 68 plasma ctDNA samples and 5 with retinoblastoma-simulating lesions. Methods The ctDNA analyzed with hybridization capture and next-generation sequencing in blood (plasma) of patients who had retinoblastoma or simulating lesions were evaluated for association with clinical course of the disease. Main Outcome Measures Presence or absence of molecular aberrations in the RB1 gene and correlations with clinical features. Results RB1 cell-free DNA (cfDNA) was detected in 16 of 19 patients with newly diagnosed, untreated intraocular retinoblastoma and in 3 of 3 patients with newly diagnosed, untreated metastatic disease. It was also present in 3 patients with recurrent intraocular disease before therapy, but was not present in patients with recurrent disease who received intra-arterial chemotherapy, nor in 21 patients who had undergone enucleation for unilateral disease. In 1 patient who had delayed treatment (insurance reasons) and showed rapid growth of the intraocular tumor, the variant allele frequency increased in 1 month from 0.34% to 2.48%. No RB1 mutations were detected in the cfDNA from plasma of patients with simulating lesions (3 with Coats disease and 1 with persistent fetal vasculature [PFV]). In 2 patients, we identified 2 independent RB1 mutations in plasma. Conclusions Mutations in RB1 were found in the cfDNA from blood of patients with newly diagnosed, untreated retinoblastoma and in patients who showed disease recurrence in the eye after prior treatment, but not in unilateral retinoblastoma after enucleation Levels of ctDNA increase in patients with progressive disease who did not receive any treatment. High plasma cfDNA levels were detected in patients with newly diagnosed metastatic disease, and these levels decreased after systemic chemotherapy was administered. Further validation is needed for measuring the somatic alterations in cfDNA from blood in retinoblastoma that could provide a promising method of monitoring patients in the future.
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Affiliation(s)
- David H. Abramson
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jasmine H. Francis
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York
| | - Ira J. Dunkel
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pediatrics, Weill Cornell Medical College, New York, New York
| | - A. Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Monica S. Diosdado
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa A. Robbins
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prachi Kothari
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dana W.Y. Tsui
- Department of Pathology, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
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30
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Prouteau A, Denis JA, De Fornel P, Cadieu E, Derrien T, Kergal C, Botherel N, Ulvé R, Rault M, Bouzidi A, François R, Dorso L, Lespagnol A, Devauchelle P, Abadie J, André C, Hédan B. Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma. Sci Rep 2021; 11:877. [PMID: 33441840 PMCID: PMC7806858 DOI: 10.1038/s41598-020-80332-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor DNA (ctDNA) has become an attractive biomarker in human oncology, and its use may be informative in canine cancer. Thus, we used droplet digital PCR or PCR for antigen receptor rearrangement, to explore tumor-specific point mutations, copy number alterations, and chromosomal rearrangements in the plasma of cancer-affected dogs. We detected ctDNA in 21/23 (91.3%) of histiocytic sarcoma (HS), 2/8 (25%) of oral melanoma, and 12/13 (92.3%) of lymphoma cases. The utility of ctDNA in diagnosing HS was explored in 133 dogs, including 49 with HS, and the screening of recurrent PTPN11 mutations in plasma had a specificity of 98.8% and a sensitivity between 42.8 and 77% according to the clinical presentation of HS. Sensitivity was greater in visceral forms and especially related to pulmonary location. Follow-up of four dogs by targeting lymphoma-specific antigen receptor rearrangement in plasma showed that minimal residual disease detection was concordant with clinical evaluation and treatment response. Thus, our study shows that ctDNA is detectable in the plasma of cancer-affected dogs and is a promising biomarker for diagnosis and clinical follow-up. ctDNA detection appears to be useful in comparative oncology research due to growing interest in the study of natural canine tumors and exploration of new therapies.
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Affiliation(s)
- Anaïs Prouteau
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Jérôme Alexandre Denis
- Sorbonne University, Paris, France.,INSERM UMR_S 938, Endocrinology and Oncology Biochemistry Department, APHP Pitié-Salpêtrière Hospital, Paris, France
| | | | - Edouard Cadieu
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Camille Kergal
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Nadine Botherel
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Ronan Ulvé
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Mélanie Rault
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | | | | | - Laetitia Dorso
- Department of Biology, Pathology and Food Sciences, Oniris, Laboniris, Nantes, France
| | - Alexandra Lespagnol
- Laboratory of Somatic Genetic of Cancers, Hospital of Rennes, Rennes, France
| | | | - Jérôme Abadie
- Department of Biology, Pathology and Food Sciences, Oniris, Laboniris, Nantes, France
| | - Catherine André
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Benoît Hédan
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France.
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Barefoot ME, Lindberg MR, Wellstein A. Decoding the Tissue of Origin of Cellular Damage from Cell-Free DNA in Liquid Biopsies. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11669-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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32
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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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A Highly Sensitive Next-Generation Sequencing-Based Genotyping Platform for EGFR Mutations in Plasma from Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2020; 12:cancers12123579. [PMID: 33266057 PMCID: PMC7760633 DOI: 10.3390/cancers12123579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary In this study, Sel-CapTM, a next-generation sequencing (NGS)-based genotyping platform, showed high sensitivity for detection of epidermal growth factor receptor (EGFR) gene mutations in plasma samples collected from 185 patients with non-small cell lung cancer (NSCLC). In the early-stage NSCLC, Sel-Cap liquid biopsy was able to detect more than half the EGFR mutations, which were detected in tumor tissue (sensitivity: 50% and 78% for Ex19del and L858R respectively, with tumor results as the references), while the conventional NGS could not detect any. Sel-Cap liquid biopsy was particularly sensitive for resistant mutation T790M (sensitivity: 88%). In addition, we conducted a retrospective study to monitor T790M using Sel-Cap in 34 patients who progressed on first-line tyrosine kinase inhibitors (EGFR-TKIs). The study suggested that the first appearance of T790M in plasma, ranging from at treatment baseline to over three years post-EGFR-TKI initiation, may be useful for prediction of disease progression (around 5 months in advance). Abstract Sel-CapTM, a digital enrichment next-generation sequencing (NGS)-based cancer panel, was assessed for detection of epidermal growth factor receptor (EGFR) gene mutations in plasma for non-small cell lung cancer (NSCLC), and for application in monitoring EGFR resistance mutation T790M in plasma following first-line EGFR-tyrosine kinase inhibitor (EGFR-TKI) treatment. Using Sel-Cap, we genotyped plasma samples collected from 185 patients for mutations Ex19del, L858R, and T790M, and compared results to those of PNAclampTM tumor biopsy (reference method, a peptide nucleic acid-mediated polymerase chain reaction clamping) and two other NGS liquid biopsies. Over two-thirds of activating mutations (Ex19del and L858R), previously confirmed by PNAclamp, were detected by Sel-Cap, which is 4–5 times more sensitive than NGS liquid biopsy. Sel-Cap showed particularly high sensitivity for T790M (88%) and for early-stage plasma samples. The relationship between initial T790M detection in plasma and progression-free survival (PFS) following first-line EGFR-TKIs was evaluated in 34 patients. Patients with T790M detected at treatment initiation (±3 months) had significantly shorter PFS than patients where T790M was first detected >3 months post treatment initiation (median PFS: 5.9 vs. 26.5 months; p < 0.0001). However, time from T790M detection to disease progression was not significantly different between the two groups (median around 5 months). In conclusion, Sel-Cap is a highly sensitive platform for EGFR mutations in plasma, and the timing of the first appearance of T790M in plasma, determined via highly sensitive liquid biopsies, may be useful for prediction of disease progression of NSCLC, around 5 months in advance.
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Jiang N, Zhou J, Zhang W, Li P, Liu Y, Shi H, Zhang C, Wang Y, Zhou C, Peng C, Zhang W, Hao Y, Sun Q, Li Y, Zhao X. RNF213 gene mutation in circulating tumor DNA detected by targeted next-generation sequencing in the assisted discrimination of early-stage lung cancer from pulmonary nodules. Thorac Cancer 2020; 12:181-193. [PMID: 33200540 PMCID: PMC7812078 DOI: 10.1111/1759-7714.13741] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 01/04/2023] Open
Abstract
Background To distinguish early‐stage lung cancer from benign disease in pulmonary nodules, especially lesions with ground‐glass opacity (GGO), we assessed gene mutations of ctDNA in peripheral blood using targeted next‐generation sequencing (NGS). Methods Single pulmonary nodule patients without mediastinal lymph nodes and symptoms that were hard to diagnose by chest CT and lung cancer biomarker measurement in multiple medical centers were enrolled into the study. All patients accepted minimally invasive surgery but refused preoperative biopsy. Gene mutations in preoperative blood samples were detected by targeted NGS. Mutations with significant differences between lung tumors and benign lesions, as grouped by postoperative pathology, were screened. Protein expression was determined by immunohistochemistry. Highly expressed genes were selected as biomarkers to verify the mutations in peripheral blood. Results In the training set, the RNF213, KMT2D, CSMD3 and LRP1B genes were mutated more frequently in early‐stage lung cancer (27 cases) than in benign nodules (15 cases) (P < 0.05). High expression of the RNF213 gene in lung cancers and low expression in benign diseases were seen by immunohistochemistry. The RNF213 gene was mutated in 25% of lung cancer samples in the validation set of 28 samples and showed high specificity (100%). In GGO patients, RNF213 was mutated more frequently in early‐stage lung cancer compared to benign diseases (P < 0.05). Conclusions RNF213 gene mutations were observed more frequently in early‐stage lung cancer, but not in benign nodules. Mutation of the RNF213 gene in peripheral blood may be a high specificity biomarker for the assisted early diagnosis of lung cancer in pulmonary nodules. Key points Significant findings of the study: In peripheral venous blood and tumor tissue, RNF213 gene mutated more frequently in lung cancer than benign pulmonary nodules. What this study adds: Detection mutation of the RNF213 gene in peripheral blood may be a high specificity method for the assisted early diagnosis of lung cancer in pulmonary nodules.
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Affiliation(s)
- Ning Jiang
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, China.,Key Laboratory of Chest Cancer, Shandong University, Jinan, China
| | - Jie Zhou
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenhao Zhang
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Peichao Li
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yu Liu
- Department of Thoracic Surgery, The 960th Hospital of People's Liberation Army of China, Jinan, China
| | - Hubo Shi
- Department of Thoracic Surgery, Shandong Provincial Chest Hospital, Jinan, China
| | - Chengke Zhang
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, China.,Key Laboratory of Chest Cancer, Shandong University, Jinan, China
| | - Yunshan Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Chengjun Zhou
- Pathology Department, The Second Hospital of Shandong University, Jinan, China
| | - Chuanliang Peng
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, China.,Key Laboratory of Chest Cancer, Shandong University, Jinan, China
| | - Weiquan Zhang
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, China.,Key Laboratory of Chest Cancer, Shandong University, Jinan, China
| | - Yingtao Hao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, China.,Key Laboratory of Chest Cancer, Shandong University, Jinan, China
| | - Qifeng Sun
- Department of Thoracic Surgery, Shandong Provincial Hospital, Jinan, China
| | - Yuliang Li
- Department of Interventional Medicine, The Second Hospital of Shandong University, Jinan, China.,Interventional Oncology Institute, Shandong University, Jinan, China
| | - Xiaogang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, China.,Key Laboratory of Chest Cancer, Shandong University, Jinan, China
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35
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Kang ASW, Bernasconi JG, Jack W, Kanavarioti A. Ready-to-use nanopore platform for the detection of any DNA/RNA oligo at attomole range using an Osmium tagged complementary probe. Sci Rep 2020; 10:19790. [PMID: 33188229 PMCID: PMC7666163 DOI: 10.1038/s41598-020-76667-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
Nanopores can serve as single molecule sensors. We exploited the MinION, a portable nanopore device from Oxford Nanopore Technologies, and repurposed it to detect any DNA/RNA oligo (target) in a complex mixture by conducting voltage-driven ion-channel measurements. The detection and quantitation of the target is enabled by the use of a unique complementary probe. Using a validated labeling technology, probes are tagged with a bulky Osmium tag (Osmium tetroxide 2,2′-bipyridine), in a way that preserves strong hybridization between probe and target. Intact oligos traverse the MinION’s nanopore relatively quickly compared to the device’s acquisition rate, and exhibit count of events comparable to the baseline. Counts are reported by a publicly available software, OsBp_detect. Due to the presence of the bulky Osmium tag, probes traverse more slowly, produce multiple counts over the baseline, and are even detected at single digit attomole (amole) range. In the presence of the target the probe is “silenced”. Silencing is attributed to a 1:1 double stranded (ds) complex that does not fit and cannot traverse this nanopore. This ready-to-use platform can be tailored as a diagnostic test to meet the requirements for point-of-care cell-free tumor DNA (ctDNA) and microRNA (miRNA) detection and quantitation in body fluids.
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Affiliation(s)
- Albert S W Kang
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | - Janette G Bernasconi
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | | | - Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA.
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Hancock KJ, Hsu W, Klimberg VS. The Clinical Versatility of Next-Generation Sequencing in Colorectal Cancer. AMERICAN JOURNAL OF BIOMEDICAL SCIENCE & RESEARCH 2020; 7:548-550. [PMID: 32924015 DOI: 10.34297/ajbsr.2020.07.001220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Next-Generation Sequencing is an evolving technology employed in the field of cancer biology. This mini review is intended as a brief overview of NGS for the clinical utility in colorectal cancer. The pathogenesis and treatment of colorectal cancer will continue to evolve as NGS is applied to more patient samples, correlating tumor biology and outcomes.
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Affiliation(s)
- Kevin J Hancock
- Department of Surgery, University of Texas Medical Branch, USA
| | - Willie Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, USA
| | - V Suzanne Klimberg
- Department of Surgery, University of Texas Medical Branch, USA.,Adjunct Professor, MD Anderson Cancer Center, USA
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37
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García-Olmo DC, Peiró-Pastor R, Picazo MG, Olmedillas-López S, García-Arranz M, Aguado B, García-Olmo D. Liquid biopsy by NGS: Differential presence of exons (DPE) is related to metastatic potential in a colon-cancer model in the rat. Transl Oncol 2020; 13:100837. [PMID: 32736333 PMCID: PMC7393324 DOI: 10.1016/j.tranon.2020.100837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 11/17/2022] Open
Abstract
Differential presence of exons (DPE) is a method of interpretation of exome sequencing, which has been proposed to design a predictive algorithm with clinical value in patients with colorectal cancer (CRC). The goal of the present study was to examine the reproducibility in a rat model of metastatic colon cancer. DHD/K12-TRb cells were injected in syngenic immunocompetent BD-IX rats. Cells were from two stocks with low and normal metastatic potential, and injected into two separate groups of rats. Five to ten weeks after injection, blood samples were taken prior euthanasia and whole exome sequencing performed. Through DPE analysis, we identified a set of exons whose differential presence in plasma allowed us to compare both groups of tumor-bearing animals. A verification test was performed to confirm that the algorithm was able to classify extracted samples into their corresponding groups of origin. The highest mean probability was 0.8954. In conclusion, the DPE analysis in tumor-bearing animals was able to discriminate between different disease status, which fully supports previous results in CRC patients.
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Affiliation(s)
- Dolores C García-Olmo
- Centre de Recerca Experimental Biomédica Aplicada (CREBA), IRBLleida, Lleida, Spain; Experimental Research Unit, University Hospital of Albacete, Spain
| | - Ramón Peiró-Pastor
- Genomics and NGS Service, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid, Spain
| | - María G Picazo
- Experimental Research Unit, University Hospital of Albacete, Spain
| | - Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
| | - Begoña Aguado
- Genomics and NGS Service, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid, Spain
| | - Damián García-Olmo
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid, Spain.
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Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
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Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
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Zhong Y, Fan Q, Zhou Z, Wang Y, He K, Lu J. Plasma cfDNA as a Potential Biomarker to Evaluate the Efficacy of Chemotherapy in Gastric Cancer. Cancer Manag Res 2020; 12:3099-3106. [PMID: 32440208 PMCID: PMC7211302 DOI: 10.2147/cmar.s243320] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/21/2020] [Indexed: 12/24/2022] Open
Abstract
Objective To investigate the clinical value of plasma cell-free DNA (cfDNA) as a potential biomarker for advanced gastric cancer (GC). Patients and Methods One hundred and six cases of advanced gastric cancer patients receiving chemotherapy were selected as study objects. Another 40 healthy volunteers were included as control groups. Plasma cfDNA concentration was detected by (SuperbDNATM) hybridization. Changes in cfDNA concentration during chemotherapy in patients with gastric cancer whose efficacy was assessed as partial response (PR), stable disease (SD) and disease progression (PD) were analyzed respectively. The relationship between the level of cfDNA and the efficacy of chemotherapy and clinical characteristics was also explored. In addition, cfDNA and other tumor markers were subjected to specificity and sensitivity analyses using ROC. Results cfDNA concentration in advanced GC patients was significantly higher than that in healthy controls (P<0.05). The concentration of plasma cfDNA in patients with PD showed an increasing trend over time. The concentration of plasma cfDNA in patients with therapeutic effect of PR decreased over time. In patients with therapeutic effect of SD, the plasma DNA concentration showed a stable trend over time. There was no significant correlation between cfDNA concentration and factors including gender, age, pathological type, CA724, CA125,CA199, AFP and CEA. ROC results showed that the area under the curve of cfDNA was larger than other tumor markers. Conclusion Plasma cfDNA concentration was significantly increased in patients with gastric cancer, and its diagnostic efficacy was superior to that of traditional tumor markers. It can be used as a tumor biomarker to monitor the efficacy of chemotherapy for gastric cancer.
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Affiliation(s)
- Yuejiao Zhong
- Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Qingyu Fan
- Xuzhou Medical University Graduate School, Xuzhou, People's Republic of China
| | - Zhaofei Zhou
- Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yajing Wang
- Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Kang He
- Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jianwei Lu
- Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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Zhang J, Zhang X, Shen S. Treatment and relapse in breast cancer show significant correlations to noninvasive testing using urinary and plasma DNA. Future Oncol 2020; 16:849-858. [PMID: 32270709 DOI: 10.2217/fon-2020-0074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: Circulating tumor DNA is promising for routine monitoring of breast cancer. Noninvasive testing allows regular probing using plasma and urine samples. Methods: Peripheral blood and simultaneous urine collection from patients were quantified. Concordance between methods were made. Serial time-point measurements were correlated to disease outcome. Results: Index measurements demonstrate over 90% concordance with biopsy. Receiver operating characteristics curves showed over 0.95 for both plasma and urine results comparing with controls. Patients with lower risk of relapse experienced greater declines in detected DNA levels. Maximal declines were registered at 4.0- and 6.8-fold for plasma and urine results, respectively. Conclusion: Measuring and monitoring DNA levels complement existing testing regimes and provides better risk profiling of patients for possible relapse.
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Affiliation(s)
- Jinling Zhang
- Department of Breast Surgery, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubeii, PR China
| | - Xueli Zhang
- Department of Breast Surgery, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubeii, PR China
| | - Shuwei Shen
- Department of Anaesthesia, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubeii, PR China
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Weiser DA, West-Szymanski DC, Fraint E, Weiner S, Rivas MA, Zhao CWT, He C, Applebaum MA. Progress toward liquid biopsies in pediatric solid tumors. Cancer Metastasis Rev 2020; 38:553-571. [PMID: 31836951 DOI: 10.1007/s10555-019-09825-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pediatric solid tumors have long been known to shed tumor cells, DNA, RNA, and proteins into the blood. Recent technological advances have allowed for improved capture and analysis of these typically scant circulating materials. Efforts are ongoing to develop "liquid biopsy" assays as minimally invasive tools to address diagnostic, prognostic, and disease monitoring needs in childhood cancer care. Applying these highly sensitive technologies to serial liquid biopsies is expected to advance understanding of tumor biology, heterogeneity, and evolution over the course of therapy, thus opening new avenues for personalized therapy. In this review, we outline the latest technologies available for liquid biopsies and describe the methods, pitfalls, and benefits of the assays that are being developed for children with extracranial solid tumors. We discuss what has been learned in several of the most common pediatric solid tumors including neuroblastoma, sarcoma, Wilms tumor, and hepatoblastoma and highlight promising future directions for the field.
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Affiliation(s)
- Daniel A Weiser
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | | | - Ellen Fraint
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | - Shoshana Weiner
- Department of Pediatrics, Weill Cornell Medical Center, New York, NY, USA
| | - Marco A Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Carolyn W T Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Mark A Applebaum
- Department of Pediatrics, The University of Chicago, 900 E. 57th St., KCBD 5116, Chicago, IL, 60637, USA.
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Hanks E, Todd H, Palarea-Albaladejo J, McNeilly TN, Britton C, Ballingall KT. A novel technique for retrospective genetic analysis of the response to vaccination or infection using cell-free DNA from archived sheep serum and plasma. Vet Res 2020; 51:9. [PMID: 32024546 PMCID: PMC7003321 DOI: 10.1186/s13567-020-0737-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/16/2020] [Indexed: 12/31/2022] Open
Abstract
Genetic variation is associated with differences in disease resistance and susceptibility among individuals within a population. To date, molecular genetic analyses of host responses have relied on extraction of genomic DNA from whole blood or tissue samples. However, such samples are not routinely collected during large-scale field studies. We demonstrate that cell-free genomic DNA (cfDNA) may be extracted and amplified from archived plasma samples, allowing retrospective analysis of host genetic diversity. This technique was also applicable to archived serum samples up to 35 years old and to different ruminant species. As proof of concept, we used this cfDNA approach to genotype the major histocompatibility complex (MHC) class II DRB1 locus of 224 Merino sheep which had participated in field trials of a commercial Haemonchus contortus vaccine, Barbervax®, in Australia. This identified a total of 51 different DRB1 alleles and their relative frequencies. This is the first study to examine host MHC diversity using DNA extracted from archived plasma samples, an approach that may be applied to retrospective analyses of genetic diversity and responses to vaccination or infection across different species and populations.
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Affiliation(s)
- Eve Hanks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK. .,SAC Consulting: Veterinary Services, SRUC Veterinary Services, Pentland Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK.
| | - Helen Todd
- Moredun Research Institute, Pentlands Science Park, Penicuik, Edinburgh, EH26 0PZ, UK
| | - Javier Palarea-Albaladejo
- Biomathematics and Statistics Scotland, JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Penicuik, Edinburgh, EH26 0PZ, UK
| | - Collette Britton
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Keith T Ballingall
- Moredun Research Institute, Pentlands Science Park, Penicuik, Edinburgh, EH26 0PZ, UK.
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Ullrich E, Heidinger P, Soh J, Villanova L, Grabuschnig S, Bachler T, Hirschböck E, Sánchez-Heredero S, Ford B, Sensen M, Rosales Rodriguez I, Schwendenwein D, Neumeister P, Zurl CJ, Krause R, Lorenz Khol J, Sensen CW. Evaluation of host-based molecular markers for the early detection of human sepsis. J Biotechnol 2020; 310:80-88. [PMID: 32017954 DOI: 10.1016/j.jbiotec.2020.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 01/18/2020] [Accepted: 01/27/2020] [Indexed: 12/12/2022]
Abstract
We have identified 24 molecular markers, based on circulating nucleic acids (CNA) originating from the human genome, which in combination can be used in a quantitative real-time PCR (qPCR) assay to identify the presence of human sepsis, starting two to three days before the first clinical signs develop and including patients who meet the SEPSIS-3 criteria. The accuracy was more than 87 % inside of the same patient cohort for which the markers were developed and up to 81 % in blind studies of patient cohorts which were not included in the marker development. As our markers are host-based, they can be used to capture bacterial as well as fungal sepsis, unlike the current PCR-based tests, which require species-specific primer sets for each organism causing human sepsis. Our assay directly uses an aliquot of cell-free blood as the substrate for the PCR reaction, thus allowing to obtain the diagnostic results in three to four hours after the collection of the blood samples.
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Affiliation(s)
- Elisabeth Ullrich
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | | | - Jung Soh
- CNA Diagnostics Inc., Suite 300, 4838 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Laura Villanova
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010, Graz, Styria, Austria
| | - Stefan Grabuschnig
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010, Graz, Styria, Austria
| | | | | | - Sara Sánchez-Heredero
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010, Graz, Styria, Austria
| | - Barry Ford
- Defence Research and Development Canada, Suffield Research Centre, Suffield, P.O. box 4000 Stn Main, T1A 8K6, Medicine Hat, Alberta, Canada
| | - Maria Sensen
- Hochstraße 12, 8076, Vasoldsberg, Styria, Austria
| | | | | | - Peter Neumeister
- Clinical Division for Hematology, Medical University of Graz, Auenbruggerplatz 38D, 8036 Graz, Styria, Austria
| | - Christoph J Zurl
- Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Auenbruggerplatz 34/II, 8036, Graz, Styria, Austria
| | - Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Styria, Austria; BioTechMed Graz, Mozartgasse 12/II, 8010, Graz, Styria, Austria
| | - Johannes Lorenz Khol
- Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Christoph W Sensen
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010, Graz, Styria, Austria; CNA Diagnostics GmbH, Parkring 18, 8074, Grambach, Styria, Austria; BioTechMed Graz, Mozartgasse 12/II, 8010, Graz, Styria, Austria.
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Extracellular DNA Containing (dG)n Motifs Penetrates into MCF7 Breast Cancer Cells, Induces the Adaptive Response, and Can Be Expressed. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:7853492. [PMID: 31781350 PMCID: PMC6874983 DOI: 10.1155/2019/7853492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/03/2019] [Indexed: 11/29/2022]
Abstract
Background Oxidized human DNA or plasmid DNAs containing human ribosomal genes can easily penetrate into the breast cancer cells MCF7 and stimulate the adaptive response induction. Plasmid DNA containing a CMV promoter, gene EGFP, and the insertion of the human ribosomal genes can be expressed. A hypothesis is proposed: these features of the ribosomal DNA are due to the presence of dGn motifs that are prone to oxidize. Methods Cells of MCF7 line were cultured with plasmids which contained a CMV promoter and gene of fluorescent protein EGFP. Genetic construction pEGFP-Gn contains pEGFP vector and a small insertion with dG11 and dG13 motifs that are inclined to oxidation. The accumulation of pEGFP and pEGFP-Gn in MCF7 (qPCR), the levels of ROS in the cells, the content of 8-oxodG in plasmids and cellular DNA (flow cytometry, immunoassay, and fluorescent microscopy), the expression of NOX4 and EGFP, the localization of NOX4 and EGFP in MCF7 (qPCR, flow cytometry, and fluorescent microscopy), and the levels of the cell DNA damage (comet assay) were analyzed. Results (dG)n insertions in the plasmid pEGFP increase the levels of ROS, the cell DNA oxidation and DNA damage, and the level of transfection of plasmid into the MCF7 cells. NOX4 participates in the oxidation of pEGFP-Gn and pEGFP. The expression of EGFP gene in MCF7 is significantly increased in case of pEGFP-Gn. Stimulation of ROS synthesis (H2O2 40 μM or 10 cGy IR) increases the level of expression of EGFP. Conclusions GC-rich DNA fragments containing dGn motifs that are inclined to oxidation penetrate into MCF7 cancer cells, stimulate the adaptive response, and can be expressed. This property of GC-rich cell-free DNA should be considered and/or could potentially be used in therapy of tumors.
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Ratner L. Biomarkers and Preclinical Models for Adult T-Cell Leukemia-Lymphoma Treatment. Front Microbiol 2019; 10:2109. [PMID: 31620102 PMCID: PMC6759749 DOI: 10.3389/fmicb.2019.02109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/27/2019] [Indexed: 11/13/2022] Open
Abstract
Adult T-cell leukemia/lymphoma (ATL) is an aggressive lymphoproliferative malignancy with a very poor prognosis. Despite several recent advances, new therapeutic approaches are critical, and this will require successful preclinical studies, including studies in ATL cell culture systems, and mouse models. Identification of accurate, reproducible biomarkers will be a crucial component of preclinical and clinical studies. This review summarizes the current state-of-the-art in each of these fields, and provides recommendations for future approaches. This problem is an important unmet need in HTLV research.
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Affiliation(s)
- Lee Ratner
- Division of Oncology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
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Kastrisiou M, Zarkavelis G, Pentheroudakis G, Magklara A. Clinical Application of Next-Generation Sequencing as A Liquid Biopsy Technique in Advanced Colorectal Cancer: A Trick or A Treat? Cancers (Basel) 2019; 11:E1573. [PMID: 31623125 PMCID: PMC6826585 DOI: 10.3390/cancers11101573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 12/24/2022] Open
Abstract
Owing to its advantages over prior relevant technologies, massive parallel or next-generation sequencing (NGS) is rapidly evolving, with growing applications in a wide range of human diseases. The burst in actionable molecular alterations in many cancer types advocates for the practicality of using NGS in the clinical setting, as it permits the parallel characterization of multiple genes in a cost- and time-effective way, starting from low-input DNA. In advanced clinical practice, the oncological management of colorectal cancer requires prior knowledge of KRAS, NRAS, and BRAF status, for the design of appropriate therapeutic strategies, with more gene mutations still surfacing as potential biomarkers. Tumor heterogeneity, as well as the need for serial gene profiling due to tumor evolution and the emergence of novel genetic alterations, have promoted the use of liquid biopsies-especially in the form of circulating tumor DNA (ctDNA)-as a promising alternative to tissue molecular analysis. This review discusses recent studies that have used plasma NGS in advanced colorectal cancer and summarizes the clinical applications, as well as the technical challenges involved in adopting this technique in a clinically beneficial oncological practice.
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Affiliation(s)
- Myrto Kastrisiou
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Zarkavelis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Pentheroudakis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - Angeliki Magklara
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Biomedical Research, Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas, 45110 Ioannina, Greece.
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Elbracht M, Meyer R, Eggermann T, Kurth I. [Rational use of genetic tests in internal medicine : Possibilities and limitations of next generation sequencing diagnostics]. Internist (Berl) 2019; 59:756-765. [PMID: 29946883 DOI: 10.1007/s00108-018-0457-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND New methods of molecular genetic diagnostics enable a more comprehensive genetic analysis of patients. OBJECTIVES Rational use and benefits of molecular genetic testing in patients with various internal diseases. METHOD Evaluation of topic-related literature, discussion of own experiences, as well as consideration of current guidelines. RESULTS New genetic tests, such as next generation sequencing (NGS), improve the diagnosis of hereditary diseases; however, the use of this technology also leads to additional findings, which must be carefully considered. CONCLUSION The rational use of genetic tests is a benefit for patients and can significantly influence the prevention and treatment of a disease. The increasing complexity of genetic findings requires interdisciplinary approaches involving human genetics, internal medicine, and other disciplines.
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Affiliation(s)
- M Elbracht
- Institut für Humangenetik, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland
| | - R Meyer
- Institut für Humangenetik, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland
| | - T Eggermann
- Institut für Humangenetik, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland
| | - I Kurth
- Institut für Humangenetik, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland.
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Afrang N, Honardoost M. Cell cycle regulatory markers in melanoma: New strategies in diagnosis and treatment. Med J Islam Repub Iran 2019; 33:96. [PMID: 31696090 PMCID: PMC6825388 DOI: 10.34171/mjiri.33.96] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 12/14/2022] Open
Abstract
Background: Melanoma has been known as an aggressive type of skin cancer in recent years. Reports have distributed the spread rate of melanoma among white skin populations. Also, many studies have mentioned several causes of melanoma. Ultraviolet radiation was represented to be the most important reason for occurrence of melanoma. However, recent studies have found that a combination of factors, such as environmental and genetic factors, can contribute to occurrence of various cancers, specifically melanoma. Methods: Different studies have been conducted on the efficacy of genetic disorders in melanoma. These surveys marked the key role of specific biomarkers in molecular and cellular processes, and investigations have found the expression of several genes in these processes. In addition, aberrant expression of these genes due to mutation and methylation can affect the whole process. Results: The expression process of these genes is regulated by microRNAs. These new biomolecules have been considered as negative regulators because of managing molecular and cellular processes. MicroRNAs are small conserved regulators attached to their targets leading to rearrangement of gene expression. Adherence of these noncoding RNAs can cause mRNA degradation or inhibit its translation. Conclusion: Recently, the application of specific genes in melanoma has been studied. In this review, the way melanoma is regulated because of these biomarkers and their demand through cell cycle in diagnosis, prognosis, and therapeutic periods was considered. Keywords: Melanoma, Biomarkers, Cell cycle, Biomolecules
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Affiliation(s)
- Negin Afrang
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Honardoost
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
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Mak DW, Li S, Minchom A. Challenging the recalcitrant disease—developing molecularly driven treatments for small cell lung cancer. Eur J Cancer 2019; 119:132-150. [DOI: 10.1016/j.ejca.2019.04.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/11/2019] [Accepted: 04/26/2019] [Indexed: 12/29/2022]
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50
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Teixeira SR, Abreu CM, Parkes L, Davies J, Yao S, Sawhney MA, Margarit L, Gonzalez D, Pinto IM, Francis LW, Conlan RS. Direct monitoring of breast and endometrial cancer cell epigenetic response to DNA methyltransferase and histone deacetylase inhibitors. Biosens Bioelectron 2019; 141:111386. [PMID: 31220725 DOI: 10.1016/j.bios.2019.111386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/23/2019] [Accepted: 05/30/2019] [Indexed: 12/19/2022]
Abstract
DNA methylation and histone deacetylation are key epigenetic processes involved in normal cellular function and tumorigenesis. Therapeutic strategies based on DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors are currently in use and under development for the treatment of cancers. Genome-wide DNA methylation profiling has been proposed for use in disease diagnosis, and histone modification profiling for disease stratification will follow suit. However, whether epigenome sequencing technologies will be feasible for rapid clinic diagnosis and patient treatment monitoring remains to be seen, and alternative detection technologies will almost certainly be needed. Here we used electrochemical impedance spectroscopy (EIS) employing a graphene-based screen-printed electrode system to directly measure global DNA methylation and histone H3 acetylation to compare non-cancer and breast cancer cell lines. We demonstrated that whilst global methylation was not useful as a differential marker in the cellular systems tested, histone H3 acetylation was effective at higher chromatin levels. Using breast and endometrial cancer cell models, EIS was then used to monitor cellular responses to the DNMT and HDAC inhibitors 5-Aza-2'-deoxycytidine and suberoylanilide hydroxamic acid in vitro, and proved very effective at detecting global cellular responses to either treatment, indicating that this approach could be useful in following treatment response to epigenetic drugs. Moreover, this work reports the first combined analysis of two epigenetic markers using a unified graphene-based biosensor platform, demonstrating the potential for multiplex analysis of both methylation and acetylation on the same sample.
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Affiliation(s)
- S R Teixeira
- College of Engineering, Swansea University, Bay Campus, Swansea, SA1 8QQ, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - C M Abreu
- International Iberian Nanotechnology Laboratory (INL), Portugal
| | - L Parkes
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - J Davies
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - S Yao
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - M A Sawhney
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - L Margarit
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Abertawe Bro Morganwg University Health Board, Princess of Wales Hospital Bridgend, UK
| | - D Gonzalez
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - I Mendes Pinto
- International Iberian Nanotechnology Laboratory (INL), Portugal
| | - L W Francis
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - R S Conlan
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK.
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